I'm really tired of checking this option manually for Xcode, which I cannot duplicate due to its size... maybe there is a way to create some kind of shortcut to launch an app (Xcode in my case) with the specific value of "Open using Rosetta"?
Note: this question relates only to Apple Silicon Macs.
Example of the "Open using Rosetta" option in Finder: 
2 Answers
LaunchServices are keeping track.
See ~/Library/Preferences/: Architectures for arm64 dictionary.
Modifying com.apple.LaunchServices.plist only works after reboot. You could call the private function _LSSetArchitecturePreferenceForApplicationURL defined in CoreServices.framework. This is what finder does when you check/uncheck "Open Using Rosetta."